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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.25.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/ampliseq analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-01-21, 15:49 CET based on data in: /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/work/f8/db336f000bc9a1e31493199e593079

        General Statistics

        Showing 0/4 rows.
        Sample NameTrimmed bases
        sampleID_1
        14.9%
        sampleID_1a
        16.1%
        sampleID_2
        11.1%
        sampleID_2a
        15.3%

        Cutadapt

        Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Created with MultiQC

        Trimmed Sequence Lengths (5')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 5' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Created with MultiQC

        nf-core/ampliseq Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/ampliseq

        Methods

        Data was processed using nf-core/ampliseq v2.13.0dev (doi: 10.5281/zenodo.1493841), (doi: 10.3389/fmicb.2020.550420) (Straub et al., 2020) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.3 (Di Tommaso et al., 2017) with the following command:

        nextflow -quiet -log /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/meta/nextflow.log run /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/main.nf -c /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/nextflow.config -c /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/nextflow.config -params-file /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/meta/params.json -ansi-log false -profile test_pplace_hmmsearch,singularity -with-trace /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/meta/trace.csv -w /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/work

        References

        • Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Front Microbiol. 2020 Oct 23;11:550420. https://doi.org/10.3389/fmicb.2020.550420
        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/ampliseq Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/ampliseq

        Main arguments

        FW_primer
        GTGYCAGCMGCCGCGGTAA
        RV_primer
        GGACTACNVGGGTWTCTAAT
        input
        https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet.tsv
        metadata
        https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Metadata.tsv
        outdir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/output

        ASV post processing

        filter_ssu
        bac

        Taxonomic database

        qiime_ref_taxonomy
        greengenes85

        ASV filtering

        min_frequency
        10
        min_samples
        2

        Downstream analysis

        tax_agglom_max
        3
        tax_agglom_min
        1

        Differential abundance analysis

        ancombc_effect_size
        1

        Pipeline summary report

        report_css
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/assets/nf-core_style.css
        report_logo
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/assets/nf-core-ampliseq_logo_light_long.png
        report_template
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/assets/report_template.Rmd

        Skipping specific steps

        skip_alpha_rarefaction
        true
        skip_dada_taxonomy
        true
        skip_fastqc
        true
        skip_qiime
        true

        Institutional config options

        config_profile_description
        Minimal test dataset to check pipeline function
        config_profile_name
        Test profile

        Other parameters

        pplace_sheet
        https://raw.githubusercontent.com/erikrikarddaniel/test-datasets/phyloplace/testdata/phylosearch_input.csv

        Core Nextflow options

        configFiles
        N/A
        containerEngine
        singularity
        launchDir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a
        profile
        test_pplace_hmmsearch,singularity
        projectDir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq
        runName
        mighty_gates
        userName
        ddl
        workDir
        /cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/ampliseq/.nf-test/tests/b466648aaf744b56dd5e781d3985022a/work

        MultiQC v1.25.1 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.